computeSCR {scp} | R Documentation

## Compute the sample over carrier ratio (SCR)

### Description

The function computes the ratio of the intensities of sample channels over the intentisty of the carrier channel for each feature. The ratios are averaged within the assay.

### Usage

    computeSCR(
      object,
      i,
      colvar,
      samplePattern,
      sampleFUN = "mean",
      carrierPattern,
      carrierFUN = sampleFUN,
      rowDataName = "SCR"
    )

### Arguments

`object` | A `QFeatures` object.
`i` | A `character()` or `integer()` indicating for which assay(s) the SCR needs to be computed.
`colvar` | A `character(1)` indicating the variable to take from `colData(object)` that gives the sample annotation.
`samplePattern` | A `character(1)` pattern that matches the sample encoding in `colvar`.
`sampleFUN` | A `character(1)` or `function` that provides the summarization function to use (eg mean, sum, media, max, ...). Only used when the pattern matches multiple samples. Default is `mean`. Note for custom function, `na.rm = TRUE` is passed to `sampleFUN` to ignore missing values, make sure to provide a function that accepts this argument.
`carrierPattern` | A `character(1)` pattern that matches the carrier encoding in `colvar`. Only one match per assay is allowed, otherwise only the first match is taken
`carrierFUN` | A `character(1)` or `function` that provides the summarization function to use (eg mean, sum, media, max, ...). Only used when the pattern matches multiple carriers. Default is the same function as `sampleFUN`. Note for custom function, `na.rm = TRUE` is passed to `carrierFUN` to ignore missing values, make sure to provide a function that accepts this argument.
`rowDataName` | A `character(1)` giving the name of the new variable in the `rowData` where the computed SCR will be stored. The name cannot already exist in any of the assay `rowData`.

### Value

A `QFeatures` object for which the `rowData` of the given assay(s) is augmented with the mean SCR.

### Examples

    data("scp1")
    scp1 <- computeSCR(scp1,
                       i = 1,
                       colvar = "SampleType",
                       carrierPattern = "Carrier",
                       samplePattern = "Blank|Macrophage|Monocyte",
                       sampleFUN = "mean",
                       rowDataName = "MeanSCR")
    ## Check results
    rowData(scp1)[[1]][, "MeanSCR"]

[Package scp version 1.4.0 Index]